From Science Daily:
Could the food we eat affect our genes? Study in yeast suggests this may be the case
“Cellular metabolism plays a far more dynamic role in the cells than we previously thought,” explains Dr Ralser. “Nearly all of a cell’s genes are influenced by changes to the nutrients they have access to. In fact, in many cases the effects were so strong, that changing a cell’s metabolic profile could make some of its genes behave in a completely different manner.
“The classical view is that genes control how nutrients are broken down into important molecules, but we’ve shown that the opposite is true, too: how the nutrients break down affects how our genes behave.”
The researchers believe that the findings may have wide-ranging implications, including on how we respond to certain drugs. In cancers, for example, tumour cells develop multiple genetic mutations, which change the metabolic network within the cells. This in turn could affect the behaviour of the genes and may explain with some drugs fail to work for some individuals.
“Another important aspect of our findings is a practical one for scientists,” explains says Dr Ralser. “Biological experiments are often not reproducible between laboratories and we often blame sloppy researchers for that. It appears however, that small metabolic differences can change the outcomes of the experiments. We need to establish new laboratory procedures that control better for differences in metabolism. This will help us to design better and more reliable experiments.”More.
Surely, this is bad news for genetic fundamentalism? The selfish gene and all that? Maybe our genes don’t even know what they are until we eat something. Or what?
See also: NatGeo interview: Plant intelligence ignored: One of the discoveries being made is that Lamarck’s theory, which was discredited for a century, is now being shown to be true.
Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!
Here’s the abstract:
The regulation of gene expression in response to nutrient availability is fundamental to the genotype–phenotype relationship. The metabolic–genetic make-up of the cell, as reflected in auxotrophy, is hence likely to be a determinant of gene expression. Here, we address the importance of the metabolic–genetic background by monitoring transcriptome, proteome and metabolome in a repertoire of 16 Saccharomyces cerevisiae laboratory backgrounds, combinatorially perturbed in histidine, leucine, methionine and uracil biosynthesis. The metabolic background affected up to 85% of the coding genome. Suggesting widespread confounding, these transcriptional changes show, on average, 83% overlap between unrelated auxotrophs and 35% with previously published transcriptomes generated for non-metabolic gene knockouts. Background-dependent gene expression correlated with metabolic flux and acted, predominantly through masking or suppression, on 88% of transcriptional interactions epistatically. As a consequence, the deletion of the same metabolic gene in a different background could provoke an entirely different transcriptional response. Propagating to the proteome and scaling up at the metabolome, metabolic background dependencies reveal the prevalence of metabolism-dependent epistasis at all regulatory levels. Urging a fundamental change of the prevailing laboratory practice of using auxotrophs and nutrient supplemented media, these results reveal epistatic intertwining of metabolism with gene expression on the genomic scale. (paywall) – Mohammad Tauqeer Alam, Aleksej Zelezniak, Michael Mülleder, Pavel Shliaha, Roland Schwarz, Floriana Capuano, Jakob Vowinckel, Elahe Radmaneshfar, Antje Krüger, Enrica Calvani, Steve Michel, Stefan Börno, Stefan Christen, Kiran Raosaheb Patil, Bernd Timmermann, Kathryn S. Lilley, Markus Ralser. The metabolic background is a global player in Saccharomyces gene expression epistasis. Nature Microbiology, 2016; 15030 DOI: 10.1038/nmicrobiol.2015.30
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